InSilicoSpectro::InSilico::AASequence - Elementary protein sequence.
use InSilicoSpectro::InSilico::AASequence;
Inherits from InSilicoSpectro::InSilico::Sequence. The AASequence class is intended to store protein sequence data.
Set to -3, -2, -1, 1, 2, or 3 in case the sequence was obtained by RNA/DNA translation.
Constructor. %h is a hash of attribute=>value pairs, $bpSeq is a BioPerl Bio::seq object, from which the attributes are copied, $Sequence and $AASequence are InSilicoSpectro::InSilico::Sequence and InSilicoSpectro::InSilico::AASequence respectively.
sequence accessor/modifier: sets sequence attribute if $val is given, returns the sequence attribute.
readingFrame accessor/modifier: sets readingFrame attribute if $val is given, returns the readingFrame attribute.
Modifications accessor/modifier: sets modifications if $modif, a reference to vector of modification names or a string is given (see Pheny::InSilico::MassCalculator::variablePeptide function for instance), returns a reference to a vector of modifications. This vector can be converted into a string for display purpose by the Pheny::InSilico::MassCalculator::modifToString function.
Accessor/modifier for modification at position $pos. Sets the modification if $modif, a string, is provided.
$pos = 0 is the N-terminal site, $pos = protein length +1 is the C-terminal site, and 1 <= $pos <= protein length correspond to amino acids.
To remove a modification set it to an empty string ''.
Returns the protein mass or undefined in case either the protein sequence is not set or there are variable modifications.
See t/InSilico/testAASequence.pl.
Alexandre Masselot, www.genebio.com
Jacques Colinge, Upper Austria University of Applied Science at Hagenberg
